Computer-Designed Proteins Recognize and Bind Small Molecules

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Computer-Designed Proteins Recognize and Bind Small Molecules

Posted by samzenpus on Wednesday September 4, 2013 @09:35PM from the building-it-better dept.

vinces99 writes "Computer-designed proteins that can recognize and interact with small biological molecules are now a reality. Scientists have succeeded in creating a protein molecule that can be programmed to unite with three different steroids. The achievement could have far wider ranging applications in medicine and other fields, according to the Protein Design Institute at the University of Washington. 'This is a major step toward building proteins for use as biosensors or molecular sponges, or in synthetic biology — giving organisms new tools to perform a task,' said one of the lead researchers, Christine E. Tinberg, a UW postdoctoral fellow in biochemistry."

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"... medicine and other fields ..." by bobthesungeek76036 · 2013-09-04 22:20 · Score: 1, Interesting

If steroids are involved maybe the baseball field???

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1. Re:"... medicine and other fields ..." by K.+S.+Kyosuke · 2013-09-05 01:26 · Score: 1
  
  If steroids are involved maybe the baseball field???
  Or perhaps fields of allergenic grasses?
  
  --
  Ezekiel 23:20
This can be the greatest breakthrough by colordev · 2013-09-04 22:26 · Score: 1, Insightful

What a clever idea! Instead of making small quite unnatural medicine molecules, how about making quite natural big medicine proteins that bind to various big and small natural targets.

Yes this may be the end of meaningful doping testing, but also the end of cancers and many auto-immune diseases.

Besides mad cow disease is already ancient history. What could possibly go wrong?
1. Re:This can be the greatest breakthrough by Thanshin · 2013-09-04 23:34 · Score: 2, Interesting
  
  It's but a minuscule tool in a field of science we know almost nothing about.
  Nothing but knowledge stops us from creating an arbitrary living creature to complete a task. In bio-engineering there's no lack of base materials, everything's done from stuff we use for food. There are also no hard limits, no speed of light that stops astronomers from studying the space; no uncertainty and size limits that stops us from verifying string theory.
  I don't see this as a breakthrough. Breakthroughs are for sciences with hard walls to break. Bio-engineering is more like a large field we've never been into.
  Let's hope they can apply this technique to something valuable PR-wise (medicine or nutrition seem the most obvious), so they are able to secure funding to keep going.
2. Re:This can be the greatest breakthrough by Anonymous Coward · 2013-09-04 23:53 · Score: 4, Insightful
  
  The speed of light does not stop astronomers from studying space. Actually, we'd know much less about our universe if light did not have that speed limit. It functions as a sort of time machine, or at least a window back in time, that we wouldn't otherwise have that lets us see the universe as it was early in it's history. Things like the red shift of faraway galaxies can be correlated with distance and provide a sense of scale that would otherwise be much more difficult to get. The fact that light has a finite speed is a very good thing for astronomy.
3. Re:This can be the greatest breakthrough by Thanshin · 2013-09-05 00:00 · Score: 1
  
  The fact that light has a finite speed is a very good thing for astronomy.
  Except from the small problem of our own race probably going extinct before we'll have time to land on a planet a couple thousand light years away.
  (Imagine where we'd be in marine biology if we could only see, but not penetrate, the surface of the sea.)
4. Re:This can be the greatest breakthrough by interkin3tic · 2013-09-05 02:18 · Score: 1
  
  Besides mad cow disease is already ancient history. What could possibly go wrong?
  Uh... were you ACTUALLY asking what could possibly go wrong? Because that's usually sarcastic.
  
  If it was sarcasm, you realize that the real danger from mad cow is economic. If people freak out and stop eating beef overnight. We could certainly stand to eat less beef, it could be better for the environment and national health, and would over the long-term probably improve the economy, (depending on what we replace it with), but if we SUDDENLY stopped eating beef nationally, that would be a severe blow to the agriculture and restaurant industries, and would have some pretty dire economic reprecussions.
  
  Anyway, I don't understand what mad cow has to do with anything either way. Less than a thousand people have died of mad cow, it's not really much of a concern for medicine.
  
  Doping testing as well. Performance enhancing drugs that are not proteins, this really doesn't immediately change anything there. Performing enhancing drugs that ARE proteins (are there any?), biologists and doctors have many tricks up our sleeves to identify proteins, so I'm not really seeing how that would change either.
5. Re:This can be the greatest breakthrough by Hatta · 2013-09-05 03:40 · Score: 2, Informative
  
  Breakthroughs are for sciences with hard walls to break.
  The protein folding problem has long been one of those hard walls. It was first identified as a problem 50 years ago.
  
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6. Re:This can be the greatest breakthrough by cellocgw · 2013-09-05 04:37 · Score: 1
  
  Besides mad cow disease is already ancient history. What could possibly go wrong?
  You wish. Regard: http://www.wdam.com/story/23346292/health-officials-investigate-mad-cow-death .
  
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7. Re:This can be the greatest breakthrough by cellocgw · 2013-09-05 04:42 · Score: 1
  
  The fact that light has a finite speed is a very good thing for astronomy.
  Except from the small problem of our own race probably going extinct before we'll have time to land on a planet a couple thousand light years away.
  So are you implying that if the planet were the same physical distance but only 10 light-years away we'd somehow be able to get there faster? I for one am at this time unaware of any propulsion system whose top speed is limited by relativity.
  
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8. Re:This can be the greatest breakthrough by colordev · 2013-09-05 05:12 · Score: 1
  
  I don't see this as a breakthrough. Breakthroughs are for sciences with hard walls to break.
  I consider this technology opening a door to a paradigm shift in many fields. As you point out, living organisms have few / if any hard limits. However, consider that a human genome has only about 20,000 protein coding genes, so there is a certain (diffuse) limit, what those genes can naturally catalyze or achieve. Yes, there are lots of special action proteins like luciferase that are beneficial to certain specific organisms. But there are also remains a wide range of reactions which don't have a good enough or utilizable / suitable natural biological 'producer'.
  
  For example almost all biological organisms do bad job in breaking poisons like dioxin. As this new technology advances it might be used for catalysing all kinds of specific reactions for which there's no actual need in 'traditional' living organisms.
9. Re:This can be the greatest breakthrough by colordev · 2013-09-05 05:37 · Score: 1
  
  Besides mad cow disease is already ancient history. What could possibly go wrong?
  Uh... were you ACTUALLY asking what could possibly go wrong? Because that's usually sarcastic.
  Yes, That was the sarcastic part.
  
  Anyway, I don't understand what mad cow has to do with anything either way.
  well try this, ... mad cow was caused by a badly formulated protein. a prion. In order to (some) proteins to fold into properly functioning proteins, cells have developed special tools... like "chaperone proteins. So if these "computer designed proteins" are to be used inside human body, 'some' might think that these a risk that scientists 'might' not understand all the important aspects of their creature; their own Frankenstein-protein.
  
  Yes, the sarcastic part was hidden under the layer of science... but this is slashdot and it's ok to do that here.
  
  The potential as doping ... well this is left as an exercise to the reader
Recognize? by Dcnjoe60 · 2013-09-04 22:45 · Score: 1

Really, proteins can recognize small biological molecules? Here I thought that proteins, like other molecules would react with other molecules in a bio-chemical reaction, but to find out that they can actually recognize other molecules is really amazing!
1. Re:Recognize? by SalafranceUnderhill · 2013-09-04 23:13 · Score: 1
  
  The parent was using the word 'recognise' in a metaphorical sense. Obviously.
2. Re:Recognize? by Thanshin · 2013-09-04 23:45 · Score: 2
  
  Really, proteins can recognize small biological molecules? Here I thought that proteins, like other molecules would react with other molecules in a bio-chemical reaction, but to find out that they can actually recognize other molecules is really amazing!
  Proteins can recognize biological molecules as much as people can recognize other people. Or do you think there's anything but biochemical reactions involved.
  I don't think there's an established limit of complexity of the biochemical reactions where we're supposed to attribute or stop attributing meaning to what's no more than a chemical inevitable consequence.
3. Re:Recognize? by chad_r · 2013-09-05 00:36 · Score: 1
  
  Really, proteins can recognize small biological molecules? Here I thought that proteins, like other molecules would react with other molecules in a bio-chemical reaction, but to find out that they can actually recognize other molecules is really amazing!
  What a pointless, unfunny comment. I don't know what a "bio-chemical reaction" is. If you mean a chemical reaction, then no, proteins do not react that way. The composition of the protein does not change, in the way that two reacting chemicals would change their bonding or electron counts. In general, the protein is simply shaped in a way that fits the molecule better than other molecules (i.e., it recognizes the molecule), holding it in place so that other reactions can happen more favorably. Metalloenzymes come closer to your notion of a chemical reaction with a protein, but the protein part of the enzyme is still there just to position the reactant close to the catalytic center.
4. Re:Recognize? by oodaloop · 2013-09-05 01:02 · Score: 1
  
  Obviously it wasn't obvious, or Dcnjoe60 wouldn't have made that comment!
  
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5. Re:Recognize? by Dcnjoe60 · 2013-09-05 01:18 · Score: 2
  
  Obviously it wasn't obvious, or Dcnjoe60 wouldn't have made that comment!
  It was obvious, however, if I want metaphorical descriptions, I can go to the regular press. But on a site that is supposed to cater to educated people (nerds per the masthead), why not use a more technical description instead of one you might find in USA Today or some other media directed to a 6th grade education? Even the word target is much more accurate than recognize.
  Time and time again, we discuss on /. the dumbing down of society, particularly in the areas of science and technology. It's just surprising to see /. contributing to that process by using metaphorical descriptions to summarize a technical article.
6. Re:Recognize? by drinkypoo · 2013-09-05 01:18 · Score: 3, Insightful
  
  Proteins can recognize biological molecules as much as people can recognize other people. Or do you think there's anything but biochemical reactions involved.
  Nonsense and bollocks. Suggesting that proteins recognize biological molecules is like suggesting that Duplo blocks recognize Lego bricks or that baking soda recognizes vinegar.
  
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7. Re:Recognize? by Dcnjoe60 · 2013-09-05 01:22 · Score: 1, Informative
  
  Really, proteins can recognize small biological molecules? Here I thought that proteins, like other molecules would react with other molecules in a bio-chemical reaction, but to find out that they can actually recognize other molecules is really amazing!
  Proteins can recognize biological molecules as much as people can recognize other people. Or do you think there's anything but biochemical reactions involved.
  I don't think there's an established limit of complexity of the biochemical reactions where we're supposed to attribute or stop attributing meaning to what's no more than a chemical inevitable consequence.
  I would like to see an explanation as to how a protein can recognize anything. Last I checked, there is not even the simplest nervous system. To recognize implies a higher brain function and if proteins have developed that, then we better all be worried. On the other hand, I do understand that proteins can be designed, as in this article, to target certain other molecules, but that is a simple chemical process.
8. Re:Recognize? by Dcnjoe60 · 2013-09-05 01:38 · Score: 1
  
  Really, proteins can recognize small biological molecules? Here I thought that proteins, like other molecules would react with other molecules in a bio-chemical reaction, but to find out that they can actually recognize other molecules is really amazing!
  What a pointless, unfunny comment. I don't know what a "bio-chemical reaction" is. If you mean a chemical reaction, then no, proteins do not react that way. The composition of the protein does not change, in the way that two reacting chemicals would change their bonding or electron counts. In general, the protein is simply shaped in a way that fits the molecule better than other molecules (i.e., it recognizes the molecule), holding it in place so that other reactions can happen more favorably. Metalloenzymes come closer to your notion of a chemical reaction with a protein, but the protein part of the enzyme is still there just to position the reactant close to the catalytic center.
  Biochemical reactions are those chemical processes necessary for life as opposed chemical reactions which include all organic and inorganic reactions. As such a biochemical reaction does not mean that the different molecules combine with each other like sodium and chloride do. Enzymes are a prime example of molecule that reacts in a biochemical reaction.
  But my actual point was with USA Today style of the description: Computer-designed proteins that can recognize and interact with small biological molecules are now a reality. Would be more accurately written as Computer-designed proteins that can target and interact with small biological molecules are now a reality.
  Yes, to some it may just be semantics, but words are important and on a news site that says it caters to nerds and presumably other intellectuals, one would hope the bar would be higher than what can be found in pop magazines and the regular media.
9. Re:Recognize? by the+gnat · 2013-09-05 03:01 · Score: 4, Informative
  
  But on a site that is supposed to cater to educated people (nerds per the masthead), why not use a more technical description instead of one you might find in USA Today or some other media directed to a 6th grade education? Even the word target is much more accurate than recognize.
  The term "recognize" is used all the time in the technical literature when discussing how proteins bind to, well, pretty much anything - DNA, small molecules, or other proteins. In fact, the abstract for the actual Nature article uses the phrase "molecular recognition". You may find this unacceptably colloquial, but it's common usage in the field at this point.
  (Yes, I am a biochemist.)
10. Re:Recognize? by Hatta · 2013-09-05 03:42 · Score: 2
  
  A protein recognizes its binding partners like a lock recognizes its key, or like your computer recognizes your password. Is the language a bit anthropomorphic? Yes. But everyone in biology knows what is meant. Your pedantry is useless and annoying.
  
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11. Re:Recognize? by Hatta · 2013-09-05 03:45 · Score: 2
  
  Oh, I should also add that everything that happens in your brain is a "simple chemical process". That includes recognition, and cognition, for that matter.
  
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12. Re:Recognize? by Daniel+Dvorkin · 2013-09-05 03:49 · Score: 2
  
  (Yes, I am a biochemist.)
  Well, then, obviously you're just part of the arrogant, insular, ivory-tower scientific priesthood, using fancy jargon to baffle and mislead people instead of terms acceptable to $RANDOM_SLASHDOT_USER! Probably to protect your revenue stream from payrolled articles and wasteful government grants, since as a scientist you spend a significant portion of your day rolling around naked on piles of money. You ivory-tower eggheads with your fancy degrees instead of real-world experience and common sense, I tell you ...
  
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13. Re:Recognize? by the+gnat · 2013-09-05 05:32 · Score: 2
  
  since as a scientist you spend a significant portion of your day rolling around naked on piles of money
  No, depending on whom you ask, I'm actually much too busy either fabricating data to support totalitarian socialist government policies, or developing new poisons for the pharmaceutical industry to exploit at public expense. Besides, we already blew most of our grant money on booze and gambling at a "conference" in Vegas last year.
14. Re:Recognize? by Daniel+Dvorkin · 2013-09-05 06:20 · Score: 1
  
  Oh, don't worry, you'll be getting another big pile of taxpayers' cash from the socialist in the White House soon enough. BTW, I'm having trouble coming up with fake results for my latest destroy-Americans'-faith-in God-and-reduce-us-all-to-the-level-of-monkeys-to-pave-the-way-for-the-commie-muslim-takeover paper in the Journal Of Evilutionary Research; got any tips?
  
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  The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
Suggestions and comments by voodoo+cheesecake · 2013-09-04 22:49 · Score: 1

An off-planet laboratory seems like an intelligent first move - a lunar-synchronous asteroid perhaps? My imaginary implications mostly point out the need for operational security - at least in practice. Who wants to bio-engineer organisms to transform mars here on earth anyway? Minimizing the oh s%^t factor should be a priority.
The article would have been much more interesting if the author(s) would have elaborated beyond "computer-designed." I mean get real down and nerdy about it! This is Slashdot, don't be shy.
1. Re:Suggestions and comments by voodoo+cheesecake · 2013-09-04 23:09 · Score: 1
  
  Define "well-sealed."
2. Re: Suggestions and comments by Anonymous Coward · 2013-09-04 23:23 · Score: 1
  
  Lots of seals. All barking in unison.
3. Re:Suggestions and comments by Thanshin · 2013-09-04 23:47 · Score: 1
  
  Define "well-sealed."
  Talking about biochemistry to the point of the creation of artificial programmable proteins?
  I'll consider "well-sealed" a lab in orbit from which nothing ever comes back, ever, under no circumstance.
4. Re:Suggestions and comments by Muad'Dave · 2013-09-04 23:59 · Score: 1
  
  ... instead of building a well-sealed building right here with real technologies ...
  Real technologies sometimes fail in the face of the unknown. The Andromeda Strain, anyone?
  
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5. Re:Suggestions and comments by Antique+Geekmeister · 2013-09-05 00:10 · Score: 1
  
  A well-sealed building, that has to be kept clean and maintained, is very much more difficult to maintain than an environment surrounded by miles of vacuum. Security can be vastly tighter, it's trivial to sterilize equipment by putting it outside for a short period and letting it cycle in the sun. Security is much easier to maintain: The spaces are small, and any personnel or equipment brought to them is recorded and measured to the gram to manage fuel and trajectories. And certain research techniques, such as electro-phoresis, are far simpler in zero gee. And if the lab is ever ruined by natural catastraphe, or a profoundly dangerous bioweapon accidentally created, it can be opened wide and left for vacuum and solar radiation to destroy.
  The potential cost of mishandling bio-weapons is so great that some extreme expense to allow critical riesearch but reduce the risk to a minimum would be quite justified, especially with the known containment failures at existing bio-labs. I've seen repeated reports of bio-lab containment failures for decades: increasing that margin of safety could be security well invested.
6. Re:Suggestions and comments by HiThere · 2013-09-05 07:18 · Score: 1
  
  Fiction isn't a good response. Particularly when there are so many good examples just lying around. Bridges that fall down. Nuclear reactors that fail. And everything in between.
  OTOH, it's too early in the state of the art to move it off planet. We aren't talking about reproducing organisms (including viruses) here. Admittely, that kind of thing IS one of their goals, but it's still a ways off. Prions aren't that infectious. You generally need to either eat them or inject them. And bacteria usually find them delicious. And prions seem to be the level they're aiming at now.
  P.S.: Prions are NECESSARY for mamalian life. Probably for chordate life, and possibly for multicellular life, but those I'm not sure of. The ones we notice are the ones that are infectiously "misfolded", but that's a VERY small minority.
  
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7. Re:Suggestions and comments by cusco · 2013-09-05 08:22 · Score: 1
  
  Just look at the last two people to die from smallpox; a journalist infected by an accidental release at a facility she was visiting, and the director of that facility who committed suicide (or was suicided) later.
  
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"Medicine and other fields": super poisons by Anonymous Coward · 2013-09-04 23:30 · Score: 4, Insightful

"Computer-designed proteins that can recognize and interact with small biological molecules are now a reality." very much reminds me of alpha-Amanitin, the super-potent poison of the death cap responsible for the vast majority of mushroom related deaths.
In fact, many if not most potent poisons are of the "binds much stronger to some vitally important molecules/enzymes than what should go there" kind.
1. Re:"Medicine and other fields": super poisons by interkin3tic · 2013-09-05 02:22 · Score: 1
  
  You pointed out two examples of strong poisons that already exist. So that's not really a unique danger there. Delivery is still the bigger issue. If you can put computer designed protein poisons in my food and get me to eat it, you could do so with natural poisons.
2. Re:"Medicine and other fields": super poisons by Anonymous Coward · 2013-09-05 02:42 · Score: 1
  
  I can put computer designed protein poisons in everybody's food (that's what genetical engineered crops are for) and have it selectively kill off Habsburgians. Which should get us rid of most European royalty. Is there a favorite race you want to see genocided? Create powerful poisons manufactured for some of their genetic traits and smuggle them into Monsanto's engineering department. Slap them with a National Security Letter, of course.
  Heck, just doing something less targeted like killing lactose intolerant people (or render them infertile) would make Caucasians healthier overall and create lots of opportunity for them to repopulate Asia.
  How many people have hay fever? Obviously, plant-produced proteins do not even need to get into the food chain in order to reach a large respirence.
  We are not just talking about creating efficient poisons, but also efficient and selective delivery. You can create poisons only affected a targeted subset of humans.
3. Re:"Medicine and other fields": super poisons by interkin3tic · 2013-09-05 03:37 · Score: 1
  
  I am paranoid about Monsanto and the government as much as the next guy on the internet, but that's way too tinfoil hat for me.
  
  First off, show me a poison that is specific enough for any ethnic group. We all have basically the same biochemistry. I've never heard of a poison that specifically works against even one SPECIES let alone one race. If you eat rat poison, you're going to die even though you're not a rat. If it's in everyone's food, it's going to have effects on everyone, and the plot will become obvious.
  
  Second, Monsanto isn't likely to let any government do that. Not because they care about the consumers' health, because they wouldn't want THEIR name associated with poisoning or genocide. Security letters be damned.
  
  Lastly, the problem in your scenario isn't ability to create a new protein, it's poisining the food chain.
4. Re:"Medicine and other fields": super poisons by dywolf · 2013-09-05 04:42 · Score: 1
  
  Right, but a computer designed custom protein would be an unknown. If they don't know to test for it, it would probably be overlooked. And theres the possibilty that a custom designed protein could be tailored specifically to you, such that we can all eat the food, and only you get affected, such as by interfering with your meds if you have any. Delivery is fairly easy. I'd put the difficulty on the getting away with it part.
  
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5. Re:"Medicine and other fields": super poisons by sjames · 2013-09-05 07:07 · Score: 1
  
  Ethnic specificity is a hard one, but there are known cases of toxins whose effects vary due to genetics.
  One popular rat poison, warfarin is now used as an anti-coagulant in humans is no longer used to kill rats because due to selection, too many rats are resistant to it's effects. Selection implies that there was a genetic variation in effect to select for.
  There are various diseases that affect different ethnic groups differently due to which variation of various receptors or enzymes are more commin but it is a statistical correlation, not a black and white division.
ads by StripedCow · 2013-09-04 23:43 · Score: 1

Buy your tap water from Google, and receive small proteins that program your brain to buy stuff.

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In other words by ThatsNotPudding · 2013-09-04 23:52 · Score: 1

A more effective bioweapon. Mr. Nobel would be so proud (as in: unintended misery loves company).
Helluva Microscope by heavyion · 2013-09-05 00:42 · Score: 1

I want a microscope like the one in the picture in the article that researcher is using to "... examine in the lab the molecule they designed ..."! He's not even using the highest power objective!
good news, bad news. by Gravis+Zero · 2013-09-05 00:54 · Score: 2

it's excellent that we are beginning to understand and build elementary biology and i want to see it go further because of all the good it can do. however, there's a "with great power comes great responsibility" aspect to all of this. we are getting ever closer to the point where this technology will be used to build the newest and deadliest weapon yet. a nuke can wipe out a large chunk of land with an explosion but a devious virus can kill an entire population with a cough.
you might be thinking this post is FUD but there is no uncertainty or doubt that when you invent a new technology, it will (foolishly) be used to make new and deadlier tools of war.
we live in interesting times.

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1. Re:good news, bad news. by interkin3tic · 2013-09-05 02:27 · Score: 2
  
  a devious virus can kill an entire population with a cough.
  There's a saying "The dumbest kidney is smarter than the smartest doctor." I took a virology course in undergrad. I quickly concluded that viruses were far more clever than any team of humans could come up with. I wouldn't worry about someone designing some amazing killer virus just yet: the US government still has smallpox hanging around. Plus, while a single nuke might only blow up a large chunk of land, there are how many thousand out there?
2. Re:good news, bad news. by marcosdumay · 2013-09-05 05:17 · Score: 1
  
  Viruses also evolved to not be too lethal.
  There are a few examples in history of some virus that didn't evolve that trait very well. Altough they don't end well for the virus, they don't end well for the people either.
  
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'This is a major step toward building proteins for by MugenEJ8 · 2013-09-05 03:29 · Score: 1

'This is a major step toward building proteins for use as biosensors or molecular sponges, or in synthetic biology — giving organisms new tools to perform a task'
I picture little protein workers entering the equivalent of the Industrial Age. Armed with their new fangled drills, excavators and assembly lines!
is this? by thoper · 2013-09-05 05:14 · Score: 1

is this the beginning of the descolada?
A huge accomplishment by FossilsFriend · 2013-09-09 08:33 · Score: 1

WOW! I am blown away! I just read the full UW News release. This is incredible. Graduated in 1979, and this was a sci-fi idea then. Congrads to all involved!